X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 14% peg8000, 0.1 M Tris, pH8.5, 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.95 α = 90
b = 127.95 β = 90
c = 73.4 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2011-06-16
Diffraction Radiation
Monochromator Protocol
double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97864 APS 19-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.25 50 99.8 0.052 0.04 -- 7.9 29510 29447 2.0 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.25 2.29 100.0 0.932 0.745 2.48 8.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.25 45.129 -- 1.89 31494 29447 1586 99.72 -- 0.2021 0.2016 0.2128 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2001 2.2711 -- 157 2636 0.3012 0.3499 -- 99.0
X Ray Diffraction 2.2711 2.3523 -- 138 2662 0.2381 0.2349 -- 100.0
X Ray Diffraction 2.3523 2.4464 -- 135 2682 0.2166 0.2408 -- 100.0
X Ray Diffraction 2.4464 2.5578 -- 156 2658 0.2178 0.2802 -- 100.0
X Ray Diffraction 2.5578 2.6926 -- 136 2679 0.2041 0.2413 -- 100.0
X Ray Diffraction 2.6926 2.8613 -- 131 2712 0.2039 0.2139 -- 100.0
X Ray Diffraction 2.8613 3.0821 -- 133 2712 0.2107 0.2406 -- 100.0
X Ray Diffraction 3.0821 3.3922 -- 153 2696 0.1962 0.2334 -- 100.0
X Ray Diffraction 3.3922 3.8828 -- 165 2734 0.1891 0.1979 -- 100.0
X Ray Diffraction 3.8828 4.891 -- 149 2768 0.174 0.1613 -- 100.0
X Ray Diffraction 4.891 45.138 -- 133 2881 0.2159 0.2283 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -5.4857
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.4857
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.9715
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.069
f_dihedral_angle_d 13.397
f_angle_d 1.106
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2496
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 80

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.1_743) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.refine: 1.7.1_743) model building
HKL-2000 data collection